1) The intent is that a single measure with different values will constitute a single measure group. For example, the window-to-wall ratio measure could be used multiple times within a single measure group with WWR values of 0.2, 0.3, 0.4, and 0.5. You would only apply one of those variations in a single design alternative since they're mutually exclusive to each other - that is you wouldn't apply a WWR of 0.2 as well as a WWR 0.3 to your building. So when you go to the second tab, you can just click the "create one of each" button to quickly create a design alternative for each WWR. Hopefully that makes sense.
2) No. The expectation is that you're running all of the design alternatives that haven't yet been run when you poke the arrow button. The select feature is really best used when running with AWS when you want to download detailed results of specific alternatives from the cloud. You can also select alternatives to clear the results, which allows you to re-run specific alternatives.
3) Yeah, that's irritating right? The reason has to do with how PAT stores results internally within a database, and how the database is updated when alternatives are added. It's strictly a limitation of how PAT was coded. We know this is something people would like changed, and it should be addressed within the next year when we re-work PAT to integrate more of the capability built into OS Server. Stay tuned!
@DavidReddy I changed your bullets to numbers for referencing in the answers.